Python: ValueError: setting an array element with a sequence

Question

I'm trying to use scikit-learn to do some ML.

I am using the preprocessing module to prep my data. The data are of type float.

From reading other questions regarding this issue: ValueError: setting an array element with a sequence, it's either due to wrong structure of my data or because my data is of type string. Neither seem to be the case here.

Please let me know if you have any idea how to solve this issue or what it even means. Thank you.

The code:

print(X)

pred_X = np.array(pred_X)
pred_Y = np.array(pred_Y)
X = np.array(X)
Y = np.array(Y)

X = preprocessing.scale(X)
pred_X = preprocessing.scale(pred_X)

print(x):

[[547180.0, 120.0, 113.0, 456701.0, 1.0, 6.43, -1.0, 0.313, 0.42, 0.267 3.0, 11800.0, 607208.0, 120.0, 113.0, 456701.0, 1.0, 0.273, 0.331, 0.154, 6.0, 10300.0, 458015.0, 113.0, 120.0, 45328 6.0, 1.0, 2.54, -1.0, 0.32, 0.443, 0.257, 3.0, 92000.0, 543685.0, 120.0, 113.0, 456701.0, 1.0, 6.43, 1.0, 0.296, 0.4, 0.234, 2.0, 8800.0, 594809.0, 475582.0, 120.0, 113.0, 456701.0, 1.0, 1.0, 0.295, 0.384, 0.264, 4.0, 7700.0], 
[547180.0, 120.0, 113.0, 456701.0, 1.0, 6.43, -1.0, 0.313, 0.42, 0.267, 3.0, 11800.0, 607208.0, 120.0, 113.0, 456701.0, 1.0, 0.273, 0.331, 0.154, 6.0, 10300.0, 458015.0, 113.0, 120.0, 453286.0, 1.0, 2.54, -1.0, 0.32, 0.443, 0.257, 3.0, 92000.0, 543685.0, 120.0, 113.0, 456701.0, 1.0, 6.43, 1.0, 0.296, 0.4, 0.234, 2.0, 8800.0, 594809.0, 435062.0, 120.0, 113.0, 456701.0, 1.0, 1.0, 0.312, 0.364, 0.154, 5.0, 6900.0], 
[547180.0, 120.0, 113.0, 456701.0, 1.0, 6.43, -1.0, 0.313, 0.42, 0.267, 3.0, 11800.0, 607208.0, 120.0, 113.0, 456701.0, 1.0, 0.273, 0.331, 0.154, 6.0, 10300.0, 458015.0, 113.0, 120.0, 453286.0, 1.0, 2.54, -1.0, 0.32, 0.443, 0.257, 3.0, 92000.0, 543685.0, 120.0, 113.0, 456701.0, 1.0, 6.43, 1.0, 0.296, 0.4, 0.234, 2.0, 8800.0, 594809.0, 446308.0, 120.0, 113.0, 456701.0, 1.0, 0.0, 0.221, 0.28e, 0.115, 8.0, 6400.0]]

The Error:

Traceback (most recent call last):
  File "sampleSVM.py", line 46, in <module>
    X = preprocessing.scale(X)
  File "/home/user/.local/lib/python3.5/site-packages/sklearn/preprocessing/data.py", line 133, in scale
    dtype=FLOAT_DTYPES)
  File "/home/user/.local/lib/python3.5/site-packages/sklearn/utils/validation.py", line 433, in check_array
    array = np.array(array, dtype=dtype, order=order, copy=copy)
ValueError: setting an array element with a sequence.

Solution

Your input array X is malformed. There are 59 elements in row 1, and 58 in rows 2 & 3. When you convert to a numpy array it becomes an array of shape (3,) with dtype=Object.

The solution is to check and fix your input data. Each row in X must be the same length.